- From: Alan Ruttenberg <alanruttenberg@gmail.com>
- Date: Sun, 21 Jan 2007 23:19:43 -0500
- To: Eric Neumann <eneumann@teranode.com>, William Bug <William.Bug@DrexelMed.edu>, June Kinoshita <junekino@media.mit.edu>, Tim Clark <twclark@nmr.mgh.harvard.edu>, public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>, Gwen Wong <wonglabow@verizon.net>
oops. Move "What I don't know:" to below "ADDL complex has_part..." Corrected message below -Alan On Jan 21, 2007, at 9:26 PM, Eric Neumann wrote: > Bill, > > I'm trying to understand the central issue here: is it that ADDL is > not a full gene product so one cannot use the Entrez URI? > I'm trying to understand this stuff too. Here's my current understanding: APP gene (for which there is an entrez gene entry)-> precursor protein (~700AA). Two proteases can cleave it into different fragments from 39-42 amino acids. These are collectively called Amyloid beta proteins. I.e. Amyloid beta is a protein family, though in different contexts it might refer to a specific member of that family. ADDLs are short oligomers of amyloid beta proteins. I've seen it said that they are made of Abeta(1-42) (i.e. the 42 AA cleavage product) > If so, why not just define the necessary set of peptides as new > URI's (in HCLS's namespace for now), with predicate ':derived_from > A-beta*56' ? > Abeta*56 is also a protein complex of Amyloid beta proteins. 56 here refers to the molecular weight in kDa. It wasn't specifically stated but it looks to me that Abeta*56 fits the definition of an ADDL. A single Abeta1-42 is about 4.5kDa, The variables are therefore a) which Abeta b) what size complex. So the relation is more like: precursor protein_gene_product_of APP Abeta derived_from precursor (in the BFO sense) ADDL complex has_part only Abeta (also some sort of cardinality specification) What I don't know: Whether APP splice form matters. How mutation matters. Whether ADDL refers specifically to Abeta1-42 complexes. What the comment about Abeta1-40 in the immunogen(epitope) field of the ADDL antibody in Alzforum means. Bill's note suggests that shorter fragments of Abeta might be consituents of ADDLs. I don't know if these are just experimental constructs or whether they occur in vivo. Whether ADDLs are always composed of multiples of a single form of abeta, or whether different species can be mixed. -Alan http://en.wikipedia.org/wiki/Amyloid_precursor_protein http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? db=PubMed&cmd=Retrieve&dopt=Citation&list_uids=16541076 http://www.pnas.org/cgi/content/full/95/11/6448 http://www.jbc.org/cgi/content/abstract/271/34/20631
Received on Monday, 22 January 2007 04:20:25 UTC